ChiRP Service
CHIRP (Chromatin Isolation by RNA Purification) is a method to detect RNA-bound DNA and protein interactions, allowing simultaneous analysis of lncRNA/circRNA, protein and DNA interactions.
Long non-coding RNAs (lncRNAs) are transcripts that are more than two hundred nucleotides long and the vast majority are located in the cell nucleus. Although lncRNAs do not encode any protein, their expression in different tissues and developmental stages remains specific and biologically important. chIRP technology (chromatin isolation by RNA purification) allows the identification of RNA-chromatin interactions on a genome-wide scale.
Non-coding RNAs (ncRNAs) often collaborate with proteins to generate complex structures and participate in cellular regulation. To unravel the composition and dynamics of non-coding RNA-protein complexes (RNP), the mass spectrometry technique ChIRP-MS was developed based on ChIRP, an RNA-directed proteomics technique (RNA-directed proteomics) that enables comprehensive identification of the binding proteins of specific non-coding RNAs.
ChIRP technology can be used to localize lncRNA/circRNA binding sites and other RNA molecules that may bind at a gene-wide scale, revealing the mechanism of lncRNA/circRNA biology located in the cell nucleus. The target RNA is pulled down by designing biotin probes that are inversely complementary to the target RNA sequence. The DNA chromosomal fragment with which it interacts is then attached to the streptavidin magnetic beads. Finally, the target RNA, DNA sequence is determined by qRT-PCR or sequencing, or the protein is determined by Western or mass spectrometry analysis.
ChIRP-seq does not require prior knowledge of the lncRNA binding domains involved in chromatin interactions. Tiling oligonucleotides across the target RNA allows all potential hybridization sites to be fully utilized, ensuring that all RNA fragments are captured. The use of the ChIRP probe can be used to localize lncRNA binding sites gene-wide as well as other RNA molecules that may be bound. In combination with proteomics techniques, the proteins bound by lncRNAs at the chromatin level can be identified.
Creative Proteomcis offers ChiRP analysis services for the study of RNA-DNA interactions, RNA-protein interactions, and DNA-protein interactions.
Advantages of Service
(1) In vivo interactions can be analyzed.
(2) The interactions among the complexes formed by RNA, protein and DNA can be studied simultaneously, and the two interactions between them can also be studied.
(3) The CHIRP-MS experiment can be used to find the proteins that bind to the target lncRNA without the limitation of lncRNA length.
(4) The interactions between circRNA and protein or DNA can be studied using CHIRP experiments.
Service Process
CHIRP-RNA
CHIRP-DNA
CHIRP-Protein
Sample Requirements
- Cells >107
- Fresh tissue: >0.5g
- RNA information, species information and ID.